[gmx-users] Regargding simulation of periodic silica surface

[Mirco Wahab]

On 12.09.2014 13:30, Sathish Kumar wrote:
> And here i attached the md.log file and em.gro file. Please once check.

I did run the SiO2 block of your .gro file through my distance
checker and it looks like you have massive overlap through
the y PBC boundary and one positional duplication:

  1709 (Si)	...  6358 (BO)	0          nm |     <-- two coordinates at 
the same location?

   363 (Si)	...  7007 (BO)	0.0222935  nm |    Y
  2846 (BO)	...  6875 (Si)	0.0286182  nm |    Y
   396 (Si)	...  7251 (BO)	0.0353554  nm |    Y
   345 (Si)	...  6971 (BO)	0.0362906  nm |    Y
  2939 (BO)	...  7018 (Si)	0.0476342  nm |    Y
   344 (Si)	...  6967 (BO)	0.055687   nm |    Y
  1625 (Si)	...  5439 (BO)	0.0573586  nm |    Y
  1643 (Si)	...  5449 (BO)	0.0588729  nm |    Y
  2183 (Si)	...  6404 (BO)	0.0593127  nm |    Y
  1590 (Si)	...  4186 (BO)	0.059716   nm |    Y
  1608 (Si)	...  4197 (BO)	0.0598749  nm |    Y
   395 (Si)	...  3077 (BO)	0.0683738  nm |    Y
   362 (Si)	...  7003 (BO)	0.0699715  nm |    Y
  1001 (Si)	...  4257 (BO)	0.0706683  nm |    Y
  1019 (Si)	...  4269 (BO)	0.0718127  nm |    Y
   377 (Si)	...  3065 (BO)	0.0724502  nm |    Y
  2155 (Si)	...  5378 (BO)	0.0726498  nm |    Y
  2199 (Si)	...  5448 (BO)	0.0736275  nm |    Y
  2184 (Si)	...  5438 (BO)	0.0739799  nm |    Y
  2168 (Si)	...  5387 (BO)	0.0742159  nm |    Y
  1002 (Si)	...  3064 (BO)	0.0759077  nm |    Y
   397 (Si)	...  7255 (BO)	0.0764789  nm |    Y
  1020 (Si)	...  3076 (BO)	0.0772658  nm |    Y
  2876 (BO)	...  6891 (Si)	0.0774145  nm |    Y
  2845 (BO)	...  6871 (Si)	0.078256   nm |    Y
  2154 (Si)	...  5376 (BO)	0.0801125  nm |    Y
  2153 (Si)	...  6402 (BO)	0.0808642  nm |    Y
   379 (Si)	...  7215 (BO)	0.0815047  nm |    Y
  2167 (Si)	...  5385 (BO)	0.0821037  nm |    Y
  2185 (Si)	...  5440 (BO)	0.0836657  nm |    Y
  2200 (Si)	...  5450 (BO)	0.0867524  nm |    Y
  2875 (BO)	...  6887 (Si)	0.0878234  nm |    Y
   343 (Si)	...  2995 (BO)	0.087972   nm |    Y
   361 (Si)	...  3006 (BO)	0.0882612  nm |    Y
  2938 (BO)	...  7014 (Si)	0.0884814  nm |    Y
   378 (Si)	...  7211 (BO)	0.0908792  nm |    Y
  1003 (Si)	...  3066 (BO)	0.0917607  nm |    Y
   985 (Si)	...  3007 (BO)	0.0943716  nm |    Y
  1021 (Si)	...  3078 (BO)	0.0945146  nm |    Y
   967 (Si)	...  2996 (BO)	0.0953992  nm |    Y

(The atom id's are 0-based)

Regards

M.